Actually, for what it's worth: in monkey, if you had surfaces as well as the whole head scan you can expand those surfaces, make segmentation volumes and use those to help clear up the really hard bit left over after BET (which is getting rid of the bits of the inside of head ventral to the brain and especially around the eye sockets. BET fundamentally assumes a roundish brain)
On 2 October 2012 18:32, Colin Reveley <[email protected]> wrote: > that's great, re: whole headthanks. Very pleased about that. Half would > not have been a problem (I could cut mine in half. Donna. Then they'd both > be in half :) indeed mirror it.) Both halves even better. thanks. > > I used bet myself, and cleaned manually. Quite some time ago. I presumed > you folks did something like that when you made the surface, but maybe > surefit works on a whole head scan. I've never tried it. > > So possibly the head extracted version I made is worth uploading, since > I'm enormously perfectionist as you know. > > I'll have to check and be sure it's perfect though ;) > > thanks again > > Colin > > On 2 October 2012 18:00, <[email protected]> wrote: > >> Send caret-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> Today's Topics: >> >> 1. Re: f99 volumes (Donna Dierker) >> 2. Re: f99 volumes (Jochen Ditterich) >> >> >> ---------- Forwarded message ---------- >> From: Donna Dierker <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Mon, 1 Oct 2012 11:09:32 -0500 >> Subject: Re: [caret-users] f99 volumes >> David might have more squirreled away on his machine somewhere, but I >> couldn't find this in sumsdb or my archives. >> >> I'm sure some labs around here -- very likely the Snyder Lab -- have used >> FSL's Brain Extraction Tool (BET) on the F99 atlas for various purposes, >> but I'm not aware that they released anything like that for public >> consumption. I do know from experience that the fractional intensity >> threshold and gradient matter. Possibly loop through several permutations >> and judge which combo you like best. >> >> There is a fullHead minc volume here: >> >> http://brainmap.wustl.edu/pub/donna/SAM/F99UA1.tar.gz >> login pub >> password download >> >> Bit it's 256x256x180 -- not 240. I don't think it's the most upstream >> volume we have, but it's the most upstream one I could find. >> >> >> On Sep 29, 2012, at 1:35 AM, Colin Reveley <[email protected]> wrote: >> >> > Two enquiries, one more important than the other. Less important first: >> > >> > 1) Is there a brain extracted version of the F99 scan anywhere (a >> reference version)? >> > >> > I did do it myself, in fact took quite some time over it as I remember, >> but maybe there is a reference version that's better. >> > >> > I want to use it for some non-linear registration research. you need to >> register things that are definitely equivalent. And extracting monkey >> perfectly isn't that easy. >> > >> > 2) More important thing: >> > >> > One thing I'll be doing is registering F99 to a T1 of the animal in the >> attached image. That animal was, I'm told, in the same place at the same >> time as F99. >> > >> > For that, I wonder if there is a copy of the entire F99 scan? >> > >> > That would have huge value to me. >> > >> > I may be quite wrong, but it's very possible the original scan was >> 256x256x240 voxels and looked a lot like the attached picture. There's no >> doubt F99 was acquired in a similar scanner because he's sitting up. I >> don't think there are that many scanners like that. And I basically reckon >> it was the same coil and same or similar sequence, but I could be totally >> off. >> > >> > F99 is a really good scan in terms of artefact, in addition to being an >> atlas reference (as is this animal, but a different kind of atlas), so if >> you did have the entire thing that would be really great. We're in the >> atlas business for a bit. Sort of. F99 would be a really nice scan to have, >> for a bunch of reasons. It's unlikely we'd ever want to do more than >> experiment with it but obviously we'd ask if we did anything worth knowing >> about. >> > >> > I guess even if the scan was like that originally it's now long gone, >> but if not....that would be lovely. >> > >> > many thanks, >> > >> > Colin R >> > >> > >> > >> > >> > <wemeetagain.png>_______________________________________________ >> > caret-users mailing list >> > [email protected] >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: Jochen Ditterich <[email protected]> >> To: <[email protected]> >> Cc: >> Date: Mon, 1 Oct 2012 10:42:56 -0700 >> Subject: Re: [caret-users] f99 volumes >> The F99 full head volume is also part of these two datasets in SumsDB: >> >> http://sumsdb.wustl.edu/sums/**archivelist.do?archive_id=** >> 684661&archive_name=MACAQUE.**LEFT_HEM.04-01-29.tar.gz<http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=684661&archive_name=MACAQUE.LEFT_HEM.04-01-29.tar.gz> >> >> http://sumsdb.wustl.edu/sums/**archivelist.do?archive_id=** >> 684673&archive_name=MACAQUE.**RIGHT_HEM.04-01-29.tar.gz<http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=684673&archive_name=MACAQUE.RIGHT_HEM.04-01-29.tar.gz> >> >> Cheers, >> >> Jochen >> >> On 10/1/2012 9:09 AM, Donna Dierker wrote: >> >>> David might have more squirreled away on his machine somewhere, but I >>> couldn't find this in sumsdb or my archives. >>> >>> I'm sure some labs around here -- very likely the Snyder Lab -- have >>> used FSL's Brain Extraction Tool (BET) on the F99 atlas for various >>> purposes, but I'm not aware that they released anything like that for >>> public consumption. I do know from experience that the fractional >>> intensity threshold and gradient matter. Possibly loop through >>> several permutations and judge which combo you like best. >>> >>> There is a fullHead minc volume here: >>> >>> http://brainmap.wustl.edu/pub/**donna/SAM/F99UA1.tar.gz<http://brainmap.wustl.edu/pub/donna/SAM/F99UA1.tar.gz>login >>> pub >>> password download >>> >>> Bit it's 256x256x180 -- not 240. I don't think it's the most >>> upstream volume we have, but it's the most upstream one I could >>> find. >>> >>> >>> On Sep 29, 2012, at 1:35 AM, Colin Reveley <[email protected]> >>> wrote: >>> >>> Two enquiries, one more important than the other. Less important >>>> first: >>>> >>>> 1) Is there a brain extracted version of the F99 scan anywhere (a >>>> reference version)? >>>> >>>> I did do it myself, in fact took quite some time over it as I >>>> remember, but maybe there is a reference version that's better. >>>> >>>> I want to use it for some non-linear registration research. you >>>> need to register things that are definitely equivalent. And >>>> extracting monkey perfectly isn't that easy. >>>> >>>> 2) More important thing: >>>> >>>> One thing I'll be doing is registering F99 to a T1 of the animal in >>>> the attached image. That animal was, I'm told, in the same place at >>>> the same time as F99. >>>> >>>> For that, I wonder if there is a copy of the entire F99 scan? >>>> >>>> That would have huge value to me. >>>> >>>> I may be quite wrong, but it's very possible the original scan was >>>> 256x256x240 voxels and looked a lot like the attached picture. >>>> There's no doubt F99 was acquired in a similar scanner because he's >>>> sitting up. I don't think there are that many scanners like that. >>>> And I basically reckon it was the same coil and same or similar >>>> sequence, but I could be totally off. >>>> >>>> F99 is a really good scan in terms of artefact, in addition to >>>> being an atlas reference (as is this animal, but a different kind >>>> of atlas), so if you did have the entire thing that would be really >>>> great. We're in the atlas business for a bit. Sort of. F99 would be >>>> a really nice scan to have, for a bunch of reasons. It's unlikely >>>> we'd ever want to do more than experiment with it but obviously >>>> we'd ask if we did anything worth knowing about. >>>> >>>> I guess even if the scan was like that originally it's now long >>>> gone, but if not....that would be lovely. >>>> >>>> many thanks, >>>> >>>> Colin R >>>> >>>> >>>> >>>> >>>> <wemeetagain.png>_____________**______________________________**____ >>>> caret-users mailing list [email protected] >>>> http://brainvis.wustl.edu/**mailman/listinfo/caret-users<http://brainvis.wustl.edu/mailman/listinfo/caret-users> >>>> >>> >>> >>> ______________________________**_________________ caret-users mailing >>> list [email protected] >>> http://brainvis.wustl.edu/**mailman/listinfo/caret-users<http://brainvis.wustl.edu/mailman/listinfo/caret-users> >>> >>> >> -- >> >> ------------------------- >> >> Jochen Ditterich, Ph.D. >> Associate Professor >> Center for Neuroscience >> University of California >> 1544 Newton Court >> Davis, CA 95618 >> USA >> >> office: +1 (530) 754-5084 >> lab: +1 (530) 754-6987 >> fax: +1 (530) 757-8827 >> >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >
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